tbuckley/cabot-search huggingface dataset:
IMMU-36. EVALUATION OF TUMOR DERIVED SERPINA3N IN EXPERIMENTAL GLIOBLASTOMA
Authors: Delaney Wolf, Katayoun Ayasoufi, Jiaying Zheng, Zachariah Tritz, Fang Jin, Michael Hansen, Aaron Johnson
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma (GBM) is an incurable brain cancer which is associated with severe peripheral immune suppression. Using experimental GBM, we recently determined that peripheral immunosuppression involves thymic atrophy, stunted T cell proliferation, and release of circulating factors that inhibit immune responses. RNA sequencing and proteomic studies have determined that transcripts and protein levels of Serpina3n are upregulated in the brain and serum of GBM patients and correlates with poor prognosis. We determined Serpina3n is a highly upregulated gene in the brain and the thymus of glioma-bearing mice using RNA sequencing technologies. Proteomic analysis of serum from glioma-bearing mice identified an upregulation of pathways associated with the extracellular expression of Serpina3n. We therefore sought to determine the role of Serpina3n in peripheral immunosuppression in GL261 glioma harboring wild type and Serpina3n knockout mice. Glioma implantation in Serpina3n knockout mice resulted in similar survival and peripheral immunosuppression compared to controls. Western blotting experiments confirmed that Serpina3n is expressed and secreted by GL261 gliomas isolated from WT and Serpina3n knockout mouse brains. Together this data suggests that tumor-derived, but not host derived, Serpina3n needs to be evaluated as a putative factor associated with peripheral immunosuppression.
DDDR-27. A PATIENT-DERIVED DRUG SCREENING PLATFORM PREDICTS RESPONSE TO TEMOZOLOMIDE AND IDENTIFIES POTENTIAL NEW TREATMENTS FOR GLIOBLASTOMA
Authors: Ioannis Ntafoulis, Anne Kleijn, Cassandra Posthoorn-Verheul, Stijn L W Koolen, Trisha Kers, Chelsea W J den Hollander, Jie Ju, Yunlei Li, Andrew P Stubbs, Clemens M F Dirven, Sieger Leenstra, Martine L M Lamfers
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND Major obstacles that have impeded the development of effective new therapies for GBM include inter- and intratumoral heterogeneity, the blood-brain-barrier and use of sub-optimal cell line-based preclinical models. Taking these hurdles into account, we have set up a patient-derived GBM drug-screening platform. We optimized protocols to improve cell culture success rate and retrospectively assessed the predictive power of our assay for patient response to TMZ. A large panel of GBM cells was screened for sensitivity to available oncological agents. Drugs of interest were selected based on favorable physicochemical properties for BBB crossing and potent activity in (a subset of) GBM cultures. Finally, we determined the success rate of performing a small-scale screen with 20 selected agents within 4 weeks of receiving tumor tissue. RESULTS By combining both CUSA and tissue piece-derived dissociation protocols, culture success increased to 95%, ensuring representation of the near-complete spectrum of GBM subtypes. Single-cell sequencing studies confirmed heterogeneity in our low-passage cell cultures. In vitro screening of TMZ on a large cohort (n = 55) identified 3 response categories (responders/intermediates/non-responders) for which Cox regression analysis revealed significantly different overall survival curves of corresponding patients. Screening of 107 FDA-approved anticancer agents on 45 GBM cultures underscored the tremendous intertumoral heterogeneity in drug sensitivities. We identified 20 potent agents each effective at clinically-achievable concentrations in (a subset of) GBM cultures and having favorable BBB penetration properties (CNS-MPO score). Screening of these agents on a per patient basis within 4 weeks of receiving tissue was successful in 18 out of 24 (75%) tested tumors. In the remaining cases the tumor cells grew very slowly and longer culture times were required. CONCLUSION Our drug screening platform offers a tool to predict TMZ response and assess sensitivity to candidate treatments, either for GBM subsets or on a per patient basis.
EOLP-02. THE EFFECT OF CLINICAL TRIAL ENROLLMENT ON SPECIALTY PALLIATIVE CARE RECEIPT IN PEDIATRIC AND YOUNG ADULT PATIENTS WITH HIGH GRADE GLIOMAS
Authors: Holly Roberts, Andrea Franson, Yujie Wang
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND Palliative care has been shown to provide numerous benefits to children with cancer. Pediatric patients with high grade glioma (HGG) are particularly well suited for early involvement of palliative care given their high symptom burden and relatively poor prognosis. However, a recent study revealed that pediatric patients with primary central nervous system malignancies missed multiple opportunities for appropriate palliative care involvement. We hypothesize that clinical trial enrollment may adversely impact palliative care involvement for children and young adults with HGG. METHODS We identified a cohort of 43 deceased patients with HGG treated at our institution. IRB exemption was obtained. For each patient, the electronic medical record was reviewed to collect demographic, diagnostic, clinical trial, treatment, and palliative care information. Statistical analysis was performed, employing Fisher exact and t tests. RESULTS Overall, 72% (31/43) of patients had at least one visit with a specialty palliative care provider. 56% (24/43) of patients enrolled in a clinical trial with HGG-directed therapy, with 71% (17/24) of patients who enrolled in a clinical trial receiving specialty palliative care compared to 74% (14/19) of patients who were not on a trial (p = 1.000). Among patients who received palliative care, there was no statistically significant difference in the timing of palliative care involvement, measured from the date of first palliative care contact to date of death, for patients who enrolled in a clinical trial (mean = 177 days) compared to those who did not (mean = 113 days, p = 0.180). CONCLUSIONS As our understanding of the genomic landscape of pediatric brain tumors increases, it can be expected that patients electing to enroll in targeted therapy clinical trials will also increase. As such, it is reassuring that our data suggest trial participation does not adversely impact the receipt of palliative care in children with HGG.
EPCO-14. ISOSCELES: AN INTEGRATIVE FRAMEWORK FOR THE PREDICTION OF TREATMENT RESISTANT GLIOBLASTOMA CELLS
Authors: Robert Suter, Anna Jermakowicz, Vasileios Stathias, Luz Ruiz, Matthew D'Antuono, Simon Kaeppeli, Grace Baker, Rithvik Veeramachaneni, Winston Walters, Maria Cepero, Sion Williams, Michael Ivan, Ricardo Komotar, Macarena De La Fuente, Jann Sarkaria, Stephan Schürer, Nagi Ayad
Journal: Neuro-Oncology (2022)

Abstract Glioblastoma (GBM) remains the most common and lethal adult primary brain cancer. Two of the most significant issues preventing the development of effective GBM treatments are inter- and intra-tumor heterogeneity. To address these issues, we developed a novel platform termed ISOSCELES (Inferred cell Sensitivity Operating on the integration of Single-Cell Expression and L1000 Expression Signatures). ISOSCELES integrates single-cell gene expression data in individual GBM tumors with perturbation-response data derived from the NIH Library of Integrated Network-Based Cellular Signatures (LINCS) L1000 dataset to predict sensitive and resistant tumor cell populations. Importantly, we analyzed the predictive power of ISOSCELES in an in vivo xenograft model and demonstrated that ISOSCELES reveals the GBM cell identities primed for lineage expansion during treatment with the aurora kinase inhibitor alisertib. These studies suggest that ISOSCELES can be used to identify sensitive and resistant cell populations to targeted therapies in GBM, which can inform treatment decisions in ongoing and future clinical trials.
DDDR-15. SPIDER VENOM MOLECULES IMPAIR HUMAN GLIOMA CELLS MIGRATION: POTENTIAL APPLICATION IN CANCER THERAPY
Authors: Natalia Barreto, Monize Valeria Ramos da Silva, Thomaz Augusto Alves da Rocha-E-Silva, Rafael Sutti, Juliana Mozer Sciani, Jose Carlos Esteves Veiga, Liana Verinaud, Joao Luiz Vitorino Araujo, Catarina Raposo
Journal: Neuro-Oncology (2022)

Abstract Gliomas correspond to approximately 80% of malignant neoplasms of the central nervous system. Due to its aggressiveness, there is a growing need to seek new strategies to control the disease. The components of spider venoms are stable peptides with high specificity against biological molecular targets of therapeutic relevance. It has already been demonstrated by our group that two subfractions (SFs) isolated from the Phoneutria nigriventer spider venom (PnV) (called SF1 and SF11) can delay the migration of glioblastoma (GB) well-established cell lineage in invasions assays. Therefore, the present study aimed to evaluate the responsiveness of samples collected from Brazilian patients with a presumptive diagnosis of glioma (high and low grades), to PnV SFs, in order to contribute to the development of new drugs. After patient consent, 13 samples were collected for cultivation and attempt to reach the tenth passage, to ensure the establishment of the lineage. Four lineages were established: J01 and N07 – glioblastoma (high grade); C03 and L09 – astrocytoma and oligodendroglioma (low grade) respectively. Cells were incubated for 48 hours with SF1 and SF11, during the scratch wound-healing assay. The results demonstrated that the SFs, mainly SF11 (which proved to be a pure peptide with 1603,88 Da, sequenced as PyrKKDKKDKFY–GLM–NH2), harmed the migration of all these samples when compared to the control group. In addition, initial data with J01 lineage demonstrated that migration was also affected during the transwell invasion assay; as well as ROCK protein, involved in control of cell migration, was decreased (demonstrated by western blot) by both SFs, suggesting that ROCK is involved in the mechanism of the components. Ongoing tests continue to establish other samples collected so that the tests described above will also be carried out. These results will contribute to the development of new therapies against these tumors. Support: FAPESP #2019/10003-3.
EPID-20. MORTALITY TRENDS IN PRIMARY MALIGNANT BRAIN AND CENTRAL NERVOUS SYSTEM TUMORS VARY BY HISTOPATHOLOGY, AGE, RACE, AND SEX
Authors: Marisa Thierheimer, Gino Cioffi, Kristin Waite, Carol Kruchko, Quinn Ostrom, Jill Barnholtz-Sloan
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND Primary malignant brain and other central nervous system tumors (BT) are rare cancers that have shown rising mortality rates in recent years. To elucidate potential factors involved in this rising death rate, we examined mortality trends for primary malignant BT in the United States (US) stratified by histopathology groupings, age, race, and sex. METHODS Mortality rates for demographic factors within primary malignant BT were generated using the Center for Disease Control’s National Vital Statistics Systems (NVSS) data from 2004 to 2018. Additionally, histopathology-specific incidence-based mortality rates were calculated using the National Cancer Institute’s Surveillance, Epidemiology, and End-Results (SEER) 18 data from 2004 to 2018. Joinpoint modeling was used to estimate mortality trends and annual percent changes (APC) with corresponding 95% confidence intervals (CI). RESULTS Overall, there was a very small increase in mortality from 2004-2018 (NVSS, APC: 0.3%, 95% CI: 0.1%-0.5%). Individuals 65+ years of age saw a small increase in mortality (NVSS, APC: 0.6%, 95% CI: 0.4%-0.9%), while changes in individuals of other ages were non-significant. Asian/Pacific Islander or American Indian/Alaskan Native had the largest increase in mortality (NVSS, APC: 1.6%, 95% CI: 0.7%-2.4%). Overall mortality trends by sex were similar. Among histopathology groupings, there was a small mortality increase in adults ages 65+ years with glioblastoma (SEER, APC: 0.5%, 95% CI: 0.1%-1.0%), while patients with other glioma and non-glioma did not show significant changes in mortality. In pediatric patients (ages 0-14 years), high-grade glioma mortality increased significantly from 2004-2015 (SEER, APC: 7.0%, 95% CI: 3.8%-10.3%) but had a non-significant decrease from 2015-2018. Pediatric patients with embryonal tumors had a significant mortality decrease between 2004 and 2018 (SEER, APC: -1.9%, 95% CI: -3.3%-0.5%). CONCLUSION Examining age, race, sex, and histopathology-specific mortality at the population level can provide important information for clinicians, researchers, and aid in public health planning.
DDDR-18. COMPREHENSIVE PROTEOMIC PROFILING OF BRAFV600E GLIOMA CELLS SHOWS UPREGULATION OF GLYCOLYSIS AND TCA CYCLE PROTEINS AFTER COMBINED MTOR AND MAP KINASE PATHWAY BLOCKADE
Authors: Lujain Alaali, Eric Raabe, Micah Maxwell, Charles Eberhart, Hui Zhang
Journal: Neuro-Oncology (2022)

Abstract Low-grade gliomas (LGG) are slow-growing tumors that affect neurologic function by pressing on the surrounding parts of the brain. Pediatric low-grade glioma (pLGG) is the most common childhood brain tumors. Patients with pLGG often have a significant life-long disabilities. The most common mutations in pLGG are in the mitogen-activated protein kinase (MAPK) pathway including tumor suppressor neurofibromin (NF1), and the oncogene BRAF. BRAF activates MEK1/2, which activates of ERK1/2, leading to tumorigenesis. BRAFV600E mutation results in the activation segment of the kinase “monomeric form of BRAF”, leading to constitutive activation of MAP kinase and mTOR pathways Combination treatment of TAK228 (mTOR inhibitor) and trametinib (MEK1/2 inhibitor), suppressed both mTOR and MAP kinase pathways and inhibited BRAFV600E glioma tumor growth. To further investigate and understand the molecular mechanism of TAK228 and trametinib combinatorial efficacy, we performed comprehensive proteomic analysis of BRAFV600E glioma tumors treated with TAK228 and trametinib. We found increased levels of many proteins in the glycolysis and TCA cycle. Specifically we found increases at the protein level in citrate synthase, aconitase and malate dehydrogenase in the TCA cycle. In glycolysis, we observed increased glucose transporter expression (SLC2A1), increased hexokinase 2, and increased GAPDH. Upregualtion of these proteins may represent attempts to bypass the effects of mTOR and MAP kinase blockade on the activity of these pathways. We are currently performing flux metabolic profiling using uniformly labeled glucose to assess the activity of the pathways after combined mTOR and MAP kinase blockade. Our results may increase our understanding of how glioma cells use glucose and how mTOR and MAP kinase pathway inhibition affects basic metabolic pathways in glioma cells.
EPCO-17. UNMASKING CLONAL EVOLUTION OF DIFFUSE INTRINSIC GLIOMA USING MULTI-MODAL GENOMIC DATA
Authors: Palak Patel, Scott Ryall, Andrei Turinsky, Robert Siddaway, Sanja Pajovic, Pawel Buczkowicz, Michael Brudno, Arun Ramani, Cynthia Hawkins
Journal: Neuro-Oncology (2022)

Abstract Diffuse intrinsic pontine glioma (DIPG) is an infiltrative incurable tumor affecting children. DIPG tumors often harbor a recurrent H3K27M mutation which leads to a global loss of H3K27me2/3 and overall DNA hypomethylation, suggesting an important role of the epigenome, and consequent transcriptome in DIPG pathogenesis. To thoroughly characterize the clonal evolution of DIPG, we collected 33 samples from 7 DIPG patients using a multi-region sampling strategy and generated whole-exome and transcriptome sequencing, and DNA methylation profiling data. Using our novel bioinformatics approach, 28 distinct tumor sub-clones were identified and characterized in our cohort of DIPG patients whilst simultaneously interrogating the tumor’s ability to migrate and disseminate. When present, initiating tumor clone (Clone 1) exclusively contained H3K27M with significant DNA methylation changes whereas the divergent clones that arise later in DIPG evolutionary trees were typically driven by the copy number aberrations. Further characterization of DIPG sub-clones identified unique gene expression profiles (i.e. cell migration and angiogenesis programs) that support and enable DIPG dissemination. In this study, we uncovered how DIPG evolves at the genetic, epigenetic, and transcriptional levels in parallel and in doing so, reveal novel evolutionary phenotypes at the sub-clonal level related to the tumor’s behavior. We are further validating these results in single-cell RNA sequencing experiments and gaining further insights into the underlying molecular mechanisms responsible for invasive and aggressive DIPG phenotypes.
DDDR-10. INHIBITING INSULIN SIGNALING REVERSES RESISTANCE TO PI3K-MTOR INHIBITORS IN AGGRESSIVE PEDIATRIC HIGH-GRADE GLIOMAS
Authors: Taylor Gatesman, Katharine Halligan, Matthew Halbert, Ann-Catherine Stanton, Andrea Cruz, Brian Golbourn, Ian F Pollack, Stephen C Mack, Sameer Agnihotri
Journal: Neuro-Oncology (2022)

Abstract Primary central nervous system (CNS) tumors are now the most common cause of childhood cancer–related deaths. Pediatric high-grade gliomas (pHGGs) are among the most lethal brain tumors with a 5-year survival rate of only 20%. MYCN pHGGs represent one subgroup with an unmet need for therapeutics. MYCN belongs to the family of MYC transcription factors that regulate numerous cancer hallmarks such as proliferation, apoptosis, and metabolism. While no direct inhibitors of MYCN are in clinical trial, current strategies focus on targeting the MYCN mediated transcriptional machinery or cell cycle regulators. Lack of relevant pHGG models for pre-clinical testing contribute to limited therapeutic efficacy. To address these knowledge gaps, we developed a novel mouse model of MYCN pHGG using the FLEx-Cre switch system, whereby neural stem cells are selectively delivered with MYCN cDNA and shRNA targeting the tumor suppressor genes p53 and Pten and form tumors in vivo. We identified that this model harbors hyper-activation of the PI3K/AKT/mTOR signaling pathway. We demonstrate that dual PI3K-mTOR blood brain barrier penetrant inhibitors are effective in reducing pHGG growth and MYCN protein levels. Because treatment-resistance is a fundamental feature of pHGGs, we developed a novel drug-resistance model of MYCN pHGG as a mechanistic tool to identify relevant resistance mechanisms. Using transcriptome analysis, we identified the insulin growth factor signaling pathway as our top mechanism of resistance. We hypothesized that MYCN is a critical driver of pHGG and can be effectively targeted via dual inhibition of PI3K-mTOR and IGF/Insulin signaling pathways. We tested next generation inhibitors of IGF and PI3K/mTOR pathways and performed genetic and pharmacological assays in our MYCN pHGG and human MYCN pHGG cells. Inhibition of both pathways in our MYCN pHGG model and human MYCN cells were synergistic, leading to significant decreases in cell growth and MYCN signaling.
EPID-03. PATHOGENIC GERMLINE MUTATIONS IN GLIOMA PATIENTS
Authors: Jacob Mandel, Ali Jalali, Akash Patel, Malcolm McDonald, Lyndsey Prather, Cassandra Helfer, Xiangjun Gu, Ethan Ludmir, A J Echeverria, Ganesh Rao, Shweta Dhar, Chris Amos
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND No consensus germline testing guidelines currently exist for glioma patients. Hence such testing is not routinely performed. The prevalence and type of germline pathogenic variants in these brain tumors remains unknown. DESIGN/ METHODS A retrospective review of patients treated at Baylor College of Medicine with paired tumor/normal sequencing using the Tempus xT tumor/normal matched approach from August 2018- April 2022 was performed. Corresponding clinical data was collected for these patients. RESULTS We identified 152 glioma patients of which 15 (9.8%) had pathogenic germline variants. Pathogenic germline variants were seen in 11/84 (13.1%) of Glioblastoma, IDH wildtype, 3/42 (7.1%) of Astrocytoma, IDH mutant and 1/26 (3.8%) of Oligodendroglioma, IDH mutant and 1p/19q co-deleted patients. Pathogenic variants in BRCA2, MUTYH and CHEK2 were seen more commonly (3/15 or 20% each). BRCA1 variants were seen in 2/15 (13%) patients, with variants in NF1, ATM, MSH2, and MSH3 occurring in one patient (7%) each. Second hit somatic variants were seen in 3/15 patients (20%). A second somatic hit was seen in NF1, MUTYH and MSH2 in one patient (7%) each. Referral to genetics was performed in 6/15 (40%) patients with pathogenic germline variants. Median overall survival was 1.6 years for glioblastoma, IDH wildtype patients with a pathogenic germline variant compared to 1.79 years for glioblastoma, IDH wildtype patients without it (p = 0.67). CONCLUSIONS Although not routinely performed in glioma patients, pathogenic germline variants occurred in ~10% of our patients. Only 40% of these patients were referred to genetics. These findings suggest a possible overlooked opportunity for determination of hereditary cancer syndromes with impact on surveillance as well as potential broader treatment options. Further research to confirm the occurrence and types of pathogenic germline variants in patients with IDH wildtype compared to IDH mutant tumors is necessary.
BIOM-43. THE GENOMIC, TRANSCRIPTOMIC, AND EPIGENOMIC LANDSCAPE OF ISOCITRATE DEHYDROGENASE WILD TYPE GLIOBLASTOMA ACROSS THE AGE CONTINUUM
Authors: Margaret Johnson, April Bell, Yajas Shah, Kayla Viets-Layng, Elizabeth Mauer, Joanne Xiu, Olivier Elemento, Michael Glantz, Phillip Walker, Clark Chen, Erin Dunbar, Ekokobe Fonkem, Santosh Kesari, Andrew Brenner, Herbert Newton, Justin Low, Ashley Sumrall, Wolfgang Korn, David Ashley, Derek Wainwright
Journal: Neuro-Oncology (2022)

Abstract BACKGROUND Older age is a poor prognostic factor for glioblastoma (GBM) patients. We tested whether the intrinsic molecular landscape of the tumor may contribute to this poor prognosis. METHODS In accordance with the 2021 WHO classification scheme, we included only isocitrate dehydrogenase (IDH) wild type GBM. Based on published literature, we defined older as age &amp;gt; 65. RNA expression, gene amplification, tumor mutational burden (TMB) and mutational profiles were analyzed in three unique datasets: Tempus (n = 1,410), Caris (n = 1,432), and TCGA (n = 557). Comparison were made between &amp;lt; 65 and ³ 65 year olds using Pearson’s Chi-squared tests, Fisher’s exact tests, or Wilcoxon rank-sum where appropriate. RESULTS From our evaluable gene sets, TERT promoter mutations were more prevalent in patients ³ 65 years old (Caris 82.64 vs 77.27%, p = 0.016; Tempus 58.0 vs 49.0%, p = 0.002). There were no significant differences in PDCD1, CD274, CD3E, TNFRSF18, CD40, CD8A, TNFRSF4, CTLA4, HAVCR2, TNFSF9, CD274, or CDKN2A; PDL-1 (by IHC); dMMR/MSI-H, TMB; CDK6 amplification, EGFR amplification, EGFR, EGFRvIII, EGFR fusions, MET fusions, PTEN, TP53, or NF-1. MGMT promoter methylation (Caris data) was more common in the older group (49.73 v 34.14%, p &amp;lt; 0.001). TGCA data demonstrated that gene expression, TMB, and methylation did not change significantly with age. Additionally, PCOLCE2 and SLC10A4 were differentially methylated, and missense mutations, of any type, were more common in the older group (p=0.006). CONCLUSION Despite worse survival outcomes for older patients with IDHwt GBM as compared to younger counterparts, the molecular landscape is similar at the genomic, transcriptomic and epigenomic levels. The key exception is TERT promoter mutations that are more common in older GBM patients. Poorer survival is therefore not likely to be attributable solely to intratumoral factors.